MolNFT v1 · #178817 · protein

Tail module of mediator complex

7JMN · Mediator of RNA polymerase II transcription subunit 5: “Tail module of mediator complex”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #178817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JMN
Type: protein
Length: 1,808 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mediator of RNA polymerase II transcription subunit 5; Mediator of RNA polymerase II…
UniProt: G0SGD2, G0SCL5, G0SEV7, G0SHL5
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 5 distinct chains · 30% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Mediator of RNA polymerase II transcription subunit 5	protein	584	42% helix, 0% strand	G0SGD2
N	Mediator of RNA polymerase II transcription subunit 14	protein	198	35% helix, 15% strand	G0SCL5
P	Mediator of RNA polymerase II transcription subunit 16	protein	810	18% helix, 15% strand	G0SEV7
O	MED15	protein	164	54% helix, 0% strand	G0SHL5
X	Unknown peptide	protein	52	6% helix, 13% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	982	0.86	0.88	119	empty
2	512	0.82	0.88	84	empty
3	543	0.81	0.88	76	empty
4	262	0.80	0.93	53	empty
5	520	0.79	0.86	62	empty

Interfaces

5 interfaces between chains.

E–P · 1946 Å² buried · 4 hydrogen bonds · protein-protein
N–O · 1154 Å² buried · 10 hydrogen bonds · protein-protein
P–X · 975 Å² buried · 3 hydrogen bonds · protein-protein
N–P · 423 Å² buried · 4 hydrogen bonds · protein-protein
P–O · 203 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7JMN · Tail module of Mediator complex · the same entry in another collection · chain E against E, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt G0SGD2
Every structure of UniProt G0SCL5
Every structure of UniProt G0SEV7
Every structure of UniProt G0SHL5
Elsewhere: RCSB PDB 7JMN · PDBe 7JMN · UniProt G0SGD2 · UniProt G0SCL5 · UniProt G0SEV7 · UniProt G0SHL5

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